Difference between revisions of "POC Conf. Call 4-19-11"

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In attendance:  
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In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG),
  
−
POC members:
+
Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab),
  
−
Absent:
+
Collaborators: none
  
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Collaborators:
 
  
  
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Acceptance of the minutes from the [[POC_Conf._Call_4-12-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_4-14-11]]? ''There were no changes, additions or deletions.''
 +
 
 +
 
 +
=Tech issues:=
 +
 
 +
'''*Update on the OBO to OWL conversion:'''
 +
 
 +
''JE now has an owl version of the live plant_ontology file that has the definitions and other information. It is available at: http://palea.cgrb.oregonstate.edu/svn/Poc/tags/live/plant_ontology.owl''
 +
 
 +
''Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.''
 +
 
 +
'''PO will host the owl file and the SSWAP components of it (?), they have software that enables us to do it. (need more accurate details)''
 +
 
 +
 
 +
'''* progress on has_parts?'''
 +
 
 +
''Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations.  The problem still exists that the annotations do not flow in the right direction. ''
 +
 
 +
''JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.''
 +
 
 +
 
 +
'''*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)'''
 +
This was discussed at the [[POC_Conf._Call_3-29-11]]
 +
 
 +
Action taken:
 +
-LC talked with CM, we all agreed that it would not be too much of an issue to do so.
 +
 
 +
-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"
 +
 
 +
-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places. 
 +
 
 +
-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
 +
 
 +
''JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.''
 +
 
 +
 
 +
'''*Review for OBO Foundry Acceptance'''
 +
 
 +
''BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks''
 +
 
 +
''Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology.  We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.''
 +
 
 +
''By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here":  [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]''
  
 
=Issues arising from last week's meeting:=
 
=Issues arising from last week's meeting:=
  
−
=New terms for Physcomitrella and related taxa (continued)=
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]==
 +
 
 +
'''current definition:''' A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
  
−
==Plant Cells==
+
Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.
  
−
Terms requested by MO:
 
  
−
===archesporial cell===
+
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
  
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We have the terms:
+
Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now.
  
−
'''female archesporial cell''' (PO:0006015): In the majority of flowering plants including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
 
  
−
'''male archesporial cell''' (PO:0006014): It undergoes periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
+
'''Proposed definition of plant embryo:''' A whole plant in the early part of a sporophytic phase after the first cell division.  
  
 +
Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.
  
  
−
Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.
+
''Proposed definition is workable for now. In the comment, we should be more specific about the end of the embryonic phase in different taxa, to the extent that we know about it. We discussed that the word 'early' is quite vague, but we can't say pre-seedling stage- restricted to seed plants''
  
−
Proposed definitions:
+
''We discussed the possibility of describing the end of the embryonic phase as 'before any organs or non-embryonic organs are formed'. Problems: Cotyledons are formed in pteridophyte embryos (and many seed plants too), and they are organs. Also, the foot in a bryophyte or pteridophyte organ.''
 +
 +
''new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.''
  
−
'''archesporial cell''' A plant cell that gives rise to a sporocyte.
 
  
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Comment: May be part of an archesporium.
+
''Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form''
  
 +
[[File:embryo terms 4-14-11.jpg]]
  
−
'''female archesporial cell''' (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.
 
  
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Comment: Found in heterosporous ferns and seed plants. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
+
'''Other issues:'''
−
+
 
 +
*on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one. Also, we need haploid embryo as child of cultured embryo?  Do haploid embryos ever form in nature? 
 +
 
 +
''We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture?  BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo", as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.'''' 
 +
 
 +
''Need to add the term: zygotic (plant) embryo, is_a plant embryo, then 'cultured zygote-derived (plant) embryo' is_a zygotic (plant) embryo, and is_a cultured embryo.''
 +
 
 +
''We will also add 'haploid embryo' (microspore-derived HE?) as child of cultured embryo. Needs to be defined. Can add the naturally arising one later if needed.''
 +
 
 +
 
 +
'''*adventitious embryo''' (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells
  
−
'''male archesporial cell''' (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.
+
Is this always true?  Need to check on it.
  
−
Comment: Male archesporial cell may undergo periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
+
''It was suggested that adventitious embryo should be a synonym for somatic embryo, or maybe a child of somatic embryo. LC pointed out that adventitious embryos are really those embryos that arise where embryos normally would not arise, i.e.: on the edges of leaves on Kalanchoe or ferns. There was general agreement on this.''
  
−
===alar cell===
+
''DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.''
 +
 
 +
''Adventitious embryo should be merged into the new term 'somatic plant embryo'  Need to work on the definition of 'somatic plant embryo'.'' 
  
−
===brachycyte===
+
''Note: BS: We need to remember to put 'plant' in the all these names.''
  
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chloronema cell - done
+
*Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.
  
−
caulonema cell - done
+
Suggest that we rework the definition of [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 sporophytic phase] with a comment about apogamy.  see SF tracker and/or future meeting:
  
−
===tmema cell===
+
==[https://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 cultured plant embryo and its children]==
  
−
===jacket layer cell===
+
'''*cultured plant embryo (PO:0000010):'''
  
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===axillary hair terminal cell===
+
Current Def’n:  In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki]  Comment: None
  
−
===axillary hair base cell===
+
Rename: cultured plant embryo (PO:0000010)
  
−
===neck canal cell===
+
Proposed def’n: A plant embryo that is grown or maintained in vitro.
  
−
===side branch initial===
+
Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).
  
 +
parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure
  
−
===Other cell types, not requested by MO:===
+
PJ:  We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there
  
−
hyrdoid
+
''see the discussion above about this''
  
−
leptoid
 
  
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rhizoid initial
+
'''*cultured somatic embryo: (PO:0000011):'''  Child of cultured plant embryo
  
−
==Plant Tissues==
+
Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.
  
−
===paraphyllium===  Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
+
Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.
  
−
Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
+
new proposed def’n: A plant embryo arising from previously differentiated somatic cells ''in vitro'', rather than from the zygote or from gametes.
  
−
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
+
''is_a: plant embryo, and need a new term "somatic (plant) embryo"''
  
−
Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
 
  
−
'''Proposed definition:''' A plant organ/portion of plant tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
+
''See new proposed definition of embryo above.''
  
−
Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==
  
−
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
+
===Definition of embryonic plant structure:===
  
 +
'''embryonic plant structure''' (PO:0025099): A plant structure that is part of an embryo.
  
−
===midrib/costa===
+
Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.
−
Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)
 
  
−
We have term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.
 
  
−
We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.
+
Changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway, because technically an embryo is an embryonic plant structure.
  
−
New child of portion of plant tissue: portion of axial tissue:
+
''We discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.''
  
 +
''Ideally, we would define embryonic plant structure as "A plant structure that is part of an embryo when a plant is in the embryonic phase," but we don't have a mechanism whereby the reasoner could infer that. Humans may know that a radicle is part of an embryo when the plant is an embryo and part of a seedling when a plant is a seedling, but the reasoner could only infer it after an annotation is made, and only if the user specified the phase that the structure was taken from. Since we can't count on that, and we don't yet have embryonic phase and seedling phase, it is not a practical solution for now.''
  
−
(also, we need to redefine phloem to be more like definition of xylem, and not based on function)
+
''An alternative solution is to specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations. We will try this, because there are only 5-10 terms where this should be necessary. We should add appropriate develops from relations (e.g., seedling radicle develops_from embyronic radicle).''
−
(need to redefine axial cell so it doesn't say vascular cell)
 
  
−
===rhizoid===
+
===Some terms were left as is_a children of embryonic plant structure:===
  
−
archesporium
+
'''embryo proper''' (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.
  
−
amphithecium
+
'''scutellum''' (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
  
−
endothecium
+
'''suspensor''' (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.
  
−
jacket layer
+
===New definitions for embryonic plant cells and tissues===
 +
Both now have cross-product definitions, and no asserted is_a children
  
−
paraphysis
+
'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3177665&group_id=76834&atid=835555 embryonic plant cell]''' (PO:0025028): A plant cell that is part of an embryo.
  
−
axilliary hair
+
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
  
−
tmema
 
  
−
=Continuing User requests: for PSO=
+
Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion
  
−
- Deal with and complete the list of user requests on SourceForge-
+
Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
+
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.
  
−
submitted by Austin Mast
 
  
−
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)  
+
'''(portion of) embryonic plant tissue''' (PO:0025233): A portion of plant tissue that is part of an embryo.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
+
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
  
−
From Tucker, 2003, Flora:
+
Should we add the '''portion of''' prefix to the name?
−
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
 
−
that two to several flowers are initiated in each bract axil rather than
 
−
just one as in a raceme. '''The cluster of flowers at each node is called a fascicle.''' The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows
 
−
'''the fascicle to be a short shoot topped by a second order inflorescence apical meristem'''. This meristem initiates
 
−
flowers in a bilaterally symmetrical order: a single abaxial flower, then
 
−
two lateral flowers, another median abaxial, then two more laterals. The
 
−
number of flowers per fascicle depends on the duration of the axillary
 
−
inflorescence apex of the short shoot, which ceases activity after
 
−
initiating the few flowers in the fascicle. No flowers are initiated
 
−
adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
 
−
Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
 
−
distinguished from a cyme in that every flower is bract subtended in a
 
−
pseudoraceme."
 
  
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'''Proppsed def:''' A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated.  Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
+
coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue.
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle] (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.
  
−
We added the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
 
  
−
Alternative is to suggest bristled to PATO
+
Here is a picture of some plant tissues, to show how it works:
  
 +
[[File:Embryonic plant structure2.jpg]]
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]
+
===Proposed changes/questions for structures that were is_a embryonic plant structure:===
  
−
'''Proppsed def:''' A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
+
''Discussion of specific terms was postponed until the next meeting. For more details please see [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-26-11#embryonic_plant_structures next week's agenda]''
  
 +
'''coleoptile''' (PO:0020033)
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
+
'''coleorhiza''' (PO:0020034)
  
−
'''Banner''' (as in a legume flower) - suggest using name 'banner petal'
+
'''hypocotyl''' (PO:0020100)
  
−
'''Proppsed def:''' A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
+
'''epicotyl''' (PO:0020035)
  
 +
'''mesocotyl''' (PO:0020037)
  
−
'''Wing''' (as in a legume flower) - suggest using name 'wing petal'
+
'''hypocotyl-root junction''' PO:0004724
  
−
'''Proppsed def:''' One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
+
'''plumule'''(PO:0020032)
  
 +
'''scutellar node''' (PO:0004708)
  
−
'''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'
+
'''embryonic root''' (PO:0000045)
  
−
Suggest three new terms:
+
'''radicle''' (PO:0020031)
  
−
'''fused petal:''' A petal that is fused to another petal.
+
'''embryonic leaf''' (PO:0006338)
  
−
Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
+
=New Physcomitrella and related terms=
 +
==Collective plant structures:==
 +
''Discussion of specific terms was postponed until the next meeting. For more details please see [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-26-11#Collective_plant_structures: next week's agenda]''
  
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]===
  
−
'''fused corolla:''' A corolla in which the petals are fused.  
+
The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems.
  
−
Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
+
'''non-vascular shoot system (PO:0030017):''' A shoot system that does not have as part vascular tissue.
  
 +
comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.
  
−
'''corolla keel:''' A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae.
 
  
−
Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
+
'''vascular shoot system (PO:0030016):'''  A shoot system that has as part vascular tissue.
  
−
==TraitNet requests==
+
comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
+
participates_in sporophytic phase, has_part vascular system
  
−
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore (PO:0030018)]===
  
−
child of stem (PO:0009047).
+
'''Proposed def.:''' A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.  
  
 +
participates_in gametophytic phase, develops_from gametophore bud
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
+
Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.
  
−
Their comment: is synonym to Tubercle
+
subset for bryophytes
  
−
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud (PO:0030026)]===
  
−
tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
+
Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
  
−
proposed def:
+
'''Proposed def'n:''' A vegetative bud that develops into a gametophore.
  
 +
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
+
participates_in gametophytic phase, has_part gametophore apical cell
  
−
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
+
synonym: brown bud
  
−
proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus (PO:0030027)]===
  
 +
'''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
  
 +
Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
+
===Other gametophyte terms===
  
−
definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
+
We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.
  
−
We could add this term as a kind of upper level bin term (similar to trichome)
+
=Upcoming meetings 2011:=
  
 +
'''[http://www.iplantcollaborative.org/2011/02/09/2011-semantic-web-workshop-june-6-7-santa-fe-nm 2011 Semantic Web Workshop] June 6th and 7th, Santa Fe, NM.
 +
'''
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.  
  
−
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
+
-JE and JP will be attending
  
 +
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
−
from Crum (2001): a cluster of fern sporangia
 
−
from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
 
  
−
Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
−
Part_of vascular leaf, has_part sporangium
+
[http://icbo.buffalo.edu ICBO]
  
 +
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
 +
along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
+
'''Full-Day Workshops Schedule:'''
  
−
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
+
'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
tendrils can derived from multiple types of structures. Suggest we make separate terms:
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
−
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
−
leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
+
- LC will attend and represent the PO. Invite other plant people?
  
−
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
 
  
−
Can add other types of tendrils if they come up or users need them.
 
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
submitted by Rich Zobel (Nov 2009)
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
==User requests still open on Source Forge; PGDSO ==
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
−
===[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]===
 
  
−
This item has been open on SF since 6/2009
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
−
I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
+
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
Suggested stages:
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
 
  
−
-tuber initiation
 
  
−
-tuber growth
+
'''* International Botanical Congress (IBC2011)'''
  
−
-tuber maturation
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
How we work these in will depend on restructuring of PGDSO
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.  
  
−
===[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]===
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.  
  
−
This is a fairly new request for terms for cotton
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
 
=Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT=
 
=Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT=

Latest revision as of 23:49, 25 April 2011

POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)


In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG),

Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab),

Collaborators: none


Acceptance of the minutes from the POC_Conf._Call_4-14-11? There were no changes, additions or deletions.


Tech issues:

*Update on the OBO to OWL conversion:

JE now has an owl version of the live plant_ontology file that has the definitions and other information. It is available at: http://palea.cgrb.oregonstate.edu/svn/Poc/tags/live/plant_ontology.owl

Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.

'PO will host the owl file and the SSWAP components of it (?), they have software that enables us to do it. (need more accurate details)


* progress on has_parts?

Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations. The problem still exists that the annotations do not flow in the right direction.

JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.


*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO) This was discussed at the POC_Conf._Call_3-29-11

Action taken: -LC talked with CM, we all agreed that it would not be too much of an issue to do so.

-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"

-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.

-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?

JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.


*Review for OBO Foundry Acceptance

BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks

Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology. We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.

By email after the call: BS sent us a link to the list of principles: [OBO_Foundry_Principles] and then CM sent:"Use the list here": [Accepted]

Issues arising from last week's meeting:

plant embryo (PO:0009009)

current definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.


This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.

Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now.


Proposed definition of plant embryo: A whole plant in the early part of a sporophytic phase after the first cell division.

Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.


Proposed definition is workable for now. In the comment, we should be more specific about the end of the embryonic phase in different taxa, to the extent that we know about it. We discussed that the word 'early' is quite vague, but we can't say pre-seedling stage- restricted to seed plants

We discussed the possibility of describing the end of the embryonic phase as 'before any organs or non-embryonic organs are formed'. Problems: Cotyledons are formed in pteridophyte embryos (and many seed plants too), and they are organs. Also, the foot in a bryophyte or pteridophyte organ.

new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.


Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form

Embryo terms 4-14-11.jpg


Other issues:

  • on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one. Also, we need haploid embryo as child of cultured embryo? Do haploid embryos ever form in nature?

We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture? BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo", as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.''

Need to add the term: zygotic (plant) embryo, is_a plant embryo, then 'cultured zygote-derived (plant) embryo' is_a zygotic (plant) embryo, and is_a cultured embryo.

We will also add 'haploid embryo' (microspore-derived HE?) as child of cultured embryo. Needs to be defined. Can add the naturally arising one later if needed.


*adventitious embryo (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells

Is this always true? Need to check on it.

It was suggested that adventitious embryo should be a synonym for somatic embryo, or maybe a child of somatic embryo. LC pointed out that adventitious embryos are really those embryos that arise where embryos normally would not arise, i.e.: on the edges of leaves on Kalanchoe or ferns. There was general agreement on this.

DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.

Adventitious embryo should be merged into the new term 'somatic plant embryo' Need to work on the definition of 'somatic plant embryo'.

Note: BS: We need to remember to put 'plant' in the all these names.

  • Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.

Suggest that we rework the definition of sporophytic phase with a comment about apogamy. see SF tracker and/or future meeting:

cultured plant embryo and its children

*cultured plant embryo (PO:0000010):

Current Def’n: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki] Comment: None

Rename: cultured plant embryo (PO:0000010)

Proposed def’n: A plant embryo that is grown or maintained in vitro.

Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).

parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure

PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there

see the discussion above about this


*cultured somatic embryo: (PO:0000011): Child of cultured plant embryo

Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.

Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.

new proposed def’n: A plant embryo arising from previously differentiated somatic cells in vitro, rather than from the zygote or from gametes.

is_a: plant embryo, and need a new term "somatic (plant) embryo"


See new proposed definition of embryo above.

embryonic plant structures

Definition of embryonic plant structure:

embryonic plant structure (PO:0025099): A plant structure that is part of an embryo.

Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.


Changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway, because technically an embryo is an embryonic plant structure.

We discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.

Ideally, we would define embryonic plant structure as "A plant structure that is part of an embryo when a plant is in the embryonic phase," but we don't have a mechanism whereby the reasoner could infer that. Humans may know that a radicle is part of an embryo when the plant is an embryo and part of a seedling when a plant is a seedling, but the reasoner could only infer it after an annotation is made, and only if the user specified the phase that the structure was taken from. Since we can't count on that, and we don't yet have embryonic phase and seedling phase, it is not a practical solution for now.

An alternative solution is to specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations. We will try this, because there are only 5-10 terms where this should be necessary. We should add appropriate develops from relations (e.g., seedling radicle develops_from embyronic radicle).

Some terms were left as is_a children of embryonic plant structure:

embryo proper (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.

scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.

suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.

New definitions for embryonic plant cells and tissues

Both now have cross-product definitions, and no asserted is_a children

embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo


Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion

Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)

Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.


(portion of) embryonic plant tissue (PO:0025233): A portion of plant tissue that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo

Should we add the portion of prefix to the name?

coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue.


Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.


Here is a picture of some plant tissues, to show how it works:

Embryonic plant structure2.jpg

Proposed changes/questions for structures that were is_a embryonic plant structure:

Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda

coleoptile (PO:0020033)

coleorhiza (PO:0020034)

hypocotyl (PO:0020100)

epicotyl (PO:0020035)

mesocotyl (PO:0020037)

hypocotyl-root junction PO:0004724

plumule(PO:0020032)

scutellar node (PO:0004708)

embryonic root (PO:0000045)

radicle (PO:0020031)

embryonic leaf (PO:0006338)

New Physcomitrella and related terms

Collective plant structures:

Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda

vascular and non-vascular shoot systems

The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems.

non-vascular shoot system (PO:0030017): A shoot system that does not have as part vascular tissue.

comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.


vascular shoot system (PO:0030016): A shoot system that has as part vascular tissue.

comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.

participates_in sporophytic phase, has_part vascular system

gametophore (PO:0030018)

Proposed def.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.

participates_in gametophytic phase, develops_from gametophore bud

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.

subset for bryophytes

gametophore bud (PO:0030026)

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A vegetative bud that develops into a gametophore.

Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part gametophore apical cell

synonym: brown bud

thallus (PO:0030027)

proposed def: A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.

Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.

Other gametophyte terms

We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.

Upcoming meetings 2011:

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.


* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?


*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.


* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT

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